2GTL

Lumbricus Erythrocruorin at 3.5A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.288 
  • R-Value Observed: 0.288 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Lumbricus erythrocruorin at 3.5 a resolution: architecture of a megadalton respiratory complex.

Royer Jr., W.E.Sharma, H.Strand, K.Knapp, J.E.Bhyravbhatla, B.

(2006) Structure 14: 1167-1177

  • DOI: https://doi.org/10.1016/j.str.2006.05.011
  • Primary Citation of Related Structures:  
    2GTL

  • PubMed Abstract: 

    Annelid erythrocruorins are highly cooperative extracellular respiratory proteins with molecular masses on the order of 3.6 million Daltons. We report here the 3.5 A crystal structure of erythrocruorin from the earthworm Lumbricus terrestris. This structure reveals details of symmetrical and quasi-symmetrical interactions that dictate the self-limited assembly of 144 hemoglobin and 36 linker subunits. The linker subunits assemble into a core complex with D(6) symmetry onto which 12 hemoglobin dodecamers bind to form the entire complex. Although the three unique linker subunits share structural similarity, their interactions with each other and the hemoglobin subunits display striking diversity. The observed diversity includes design features that have been incorporated into the linker subunits and may be critical for efficient assembly of large quantities of this complex respiratory protein.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA. william.royer@umassmed.edu


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular globin 4
A, E, I
151Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P13579 (Lumbricus terrestris)
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UniProt GroupP13579
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular globin 2
B, F, J
145Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P02218 (Lumbricus terrestris)
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UniProt GroupP02218
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular globin-3
C, G, K
153Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for P11069 (Lumbricus terrestris)
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UniProt GroupP11069
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin chain d1
D, H, L
140Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for O61233 (Lumbricus terrestris)
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UniProt GroupO61233
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin linker chain L1217Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for Q9GV76 (Lumbricus terrestris)
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UniProt GroupQ9GV76
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular hemoglobin linker L2 subunit220Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for Q2I743 (Lumbricus terrestris)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Extracellular hemoglobin linker L3 subunit215Lumbricus terrestrisMutation(s): 0 
UniProt
Find proteins for Q2I742 (Lumbricus terrestris)
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
EA [auth H]
GA [auth I]
IA [auth J]
AA [auth F],
CA [auth G],
EA [auth H],
GA [auth I],
IA [auth J],
KA [auth K],
MA [auth L],
Q [auth A],
S [auth B],
U [auth C],
W [auth D],
Y [auth E]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ZN
Query on ZN

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PA [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

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NA [auth M],
OA [auth M],
QA [auth N],
RA [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CMO
Query on CMO

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
FA [auth I]
HA [auth J]
JA [auth K]
BA [auth G],
DA [auth H],
FA [auth I],
HA [auth J],
JA [auth K],
LA [auth L],
P [auth A],
R [auth B],
T [auth C],
V [auth D],
X [auth E],
Z [auth F]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.288 
  • R-Value Observed: 0.288 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.08α = 89.69
b = 257.96β = 97.15
c = 436.53γ = 90.98
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary